abyss-fixmate: error: All reads are mateless

[Chris Plott]

Hello,

I am attempting to assemble a 4 Giga base genome with ABySS version 1.3.6. I am using 9 fragment libraries. I received the following error:

"abyss-fixmate: error: All reads are mateless. This can happen when first and second read IDs do not match."

error: `AGTA_4-6.hist': No such file or directory

make: *** [AGTA_4-6.dist.dot] Error 1

make: *** Deleting file `AGTA_4-6.dist.dot'

make: *** Waiting for unfinished jobs….

I have checked the names in the files in question. All the reads are paired and are formatted as follows:

>M00949_7_000000000_A3H0P_1_1101_14037_1320/1
AACTGTTTTGAGTTACAACTTATTACAAGTGAAATTTACATCACCGAAATATTAACTGTAGCATTCTGAAAATGAGAAAATGATATTGTATCATTGATTTTCGTCATTTCTCATTCAATACGGCAACCGATTTGTAAATTGGGTTTGAGAATTCTGAGTTTCCTTTGGTGCTTGGAAAAGGCTTTTCTTTTCCCCGCTTGAGTTTGATTGTGGATATTTAGATTCCTTTCTCTATAATATTCTTGCGTG
>M00949_7_000000000_A3H0P_1_1101_14139_1320/1
CAAATTATTGCGTCTAATGCTCTTCAGAATAACCAAATAGCCGCTAGACATCTTGAGAACGCCTTCTCTAAGAATCCCTCTAAGGCCCTCTGCTTTCAAGCTTCAACTAAGACTATATTCTTCGTTATATTAGGAATATATCTCACCTCCTTCAACTCTTTTAATGTCCCGTAATACACCTTGATACAAATTGTACCCGTACCAACCAACCGGCATGTGTGATCATCTCCCATTGACATCAAATCGCCA
>M00949_7_000000000_A3H0P_1_1101_16328_1320/1
GCACTAAGCATCATACCTCGCCGGGTCATGCAATTTCTGGGCATTCCTACCCATCGTCTGAGCCCTACCCAGACGACTATTTATGGGTTTAATGCCAACAGCTCCCGCCCGATGGGGAAGATCAAGCTCAAATGCCGGATCGGGAGCCTCAAATCAGAAGTAACGTGTTACGTCATTGACGCTGACACGTCTTACAACCTGTTGCTGGGACGACCATGGATTCACCAAAATTCCATTGTTCCCTCCACTC

>M00949_7_000000000_A3H0P_1_1101_14037_1320/2
ATTTGAACTTGGCAAAGATTTATATAACCTTTTCATTTTTTTAATTTTTTGAGAAACAGATAGAAGTCACCCTTCAACCTATAACGATCTATAAAACCAATCTCAAAGATTTGTGACTGTTTTTGAATTTACAAATTATAAAATGATGACCAAACTGATAAACAATTTAAATTTCACGCAAGAATATTATAGAGAA
>M00949_7_000000000_A3H0P_1_1101_14139_1320/2
TCAATAAGTCGAAGAAGGAGTCACGATCAGAGGCCAATGTCATGAGGTTAGATGATAATGATTCTAACTCTTCTTTCTTTTCACTTTCTATTACACCATCAGGTTGTCATTCAGATGCGTCTGAGTGGGTATTGGATATGGGCTCCATCTGCCACATTCGTCCTAGAAGGGAGT
>M00949_7_000000000_A3H0P_1_1101_16328_1320/2
TCCTCAGGCTCGACGTCAGCTTCATTACCAGAGTCTGGCTCCTCTGGTTGCGGGGTTTCATTAGTCTCCTCATATAAGAGGGAATCCGTGAAGTAATTCTCGACCCCTTTGAACGGATGCCTTTCGGCAATCAACGTTCGGACCTGTCCGCTCTCGTC

When I removed this library from the next attempt I got the same error on the next library in the list. I am not sure what is causing the error, any help you could give me would be greatly appreciated. 

Regards

Chris Plott

cpl...@hudsonalpha.org

[Anthony Raymond]

Hi Chris,

Have you ever been able to run ABySS? The read IDs you pasted into your message seem fine to me.

Please send me the whole log file, along with the command you used to generate the error.

Thanks,

Tony

--
You received this message because you are subscribed to the Google Groups "ABySS" group.
To unsubscribe from this group and stop receiving emails from it, send an email to abyss-users...@googlegroups.com.
For more options, visit https://groups.google.com/d/optout.

[Florentine Scharf]

Hello,

I am wondering if the problem could have been solved?

I am facing a similar situation, however with ABySS version 1.5.2.

The input files' beginnings look like this:

head reads1.fq

@M00874:53:000000000-A6FP0:1:1101:20964:1489/1 

TGCTGCACGCCCTCCACCAGCGCTTCCGACTTGGTTTCTCTGGTCTGATGTACGAGGTGCTAAAGAACTGTCCGGGGTTGTTGGGTTACACATTGGATGTCTTCTGGTCCGGGCGTGCCGCGCTTATGGACTTGCGAGGTGGTGCACCACGGCTGATGCAATGGAGTGGCACACATCCCCTGCTTCGAAGCTATGTCCCGAGCGAACTTTTTGCGGACCTGCCCCAGCGAAATTACCTTCTGCGGAATCCGCCTGAAGCGCGGATGCGACTTGTAG

+
CBCC9FGFGDFGGGGGGGGGGGGGGDGGGGGGGGGGFF@FGCFGGGGGGGGGGFGGGGFEGGGDFGDFGGGFGGGGGGGGG@CGGFGGGGGGGGFGGGGGGGGFGGFEFBGGGGGDFGGGGDDGGGGGGGFGFFFGGGGEGGEG:DD<EFCFDG@FGGGCCFF:F7EG>GGFGGGFGFGGGG5,>ECFFEECF,++5<9:C*1**2>F7+;CGFD:/>)2**9C37*97D>BGFF=FFF?684;>D3>FF58(,()58?>616(-477:>0:2444
@M00874:53:000000000-A6FP0:1:1101:10229:1535/1
CGAGGCCCACAGAGAGGGATGTCATCAACCACACACTACAGTGCGGTCTAAACGTGGTGTTACAGTGGTCAAAAGAGTACTTCATGTCTGTCAACGTAGCGAAAACGAAGTGCACACTCTTCGGATGTATAGAGCGCCACCCCCTTACATTACAACTGGACGGCGAAAGAATAGGAGCTGACAGGACACCGAAGCTTCTAGGAGTAACATTCCAGTGTCTGCAGGGGATGGCAACACATGCGGCCGAAACGAGACGCAAGATGGACTTCCGACTACTGCAGATAG
+
CCCCCGGGGGGGGGGGGGGGGGGGFGGGGGGGGGEGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGEDCCFGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGDGGGGGGGDEGGCFCFFGGGGGGDCFGGGGGGGGGGFGGGGGGGGGGGGCEGGGGGGFGGGGGGGGGGGGGGGGGGCEFGG9EGGFGGFGGGFFGDGGGCFGGGGGGGGGGGD35CFFFFFA6FF@B@FFFFBFB>FFF>9BF:B64<?><<)41>>27489A:B?A4

head reads2.fq
@M00874:53:000000000-A6FP0:1:1101:20964:1489/2
CACCCCAGAAACTGCTACGGCGCGCAGAAGCAGCGCCCCATGCAGAAGCACACGCAATGCATCACGTTTGCGCACGCTTGTTGTACCCATCGGACTCACAACGGCACAGTACTCAGACCACACTTCGCCCCAAGCCCTTACGANNGGTGTCTCCCGAGGAGATTCCAAGGAATCCTGATGAGAAAATATGGTAAAGAGCGCAAATGGATGGACCCGACAGGCCGTG
+
CCCCCFGGGFGGGGGEGG@7FCG@:FGFG8C@ACFC@EEFGGGGGGGGC<EFGCGEGFFFA@FCFFFGGGFC@FGGG@:BFAGGGGGGGEFFGGGEEGGGDG744@FGGGGC9EF=:=FEC==8E98@C>@BEFGC6DBFFF:##55>FG8,=;DCEDE>EG6B7=E72=*2<C<7787CC*=CFC+?C:81BFF=+;>)5>EBACFA6;3AF5=.>BEB>:3:83
@M00874:53:000000000-A6FP0:1:1101:10229:1535/2
GGGAATGTAGGGCTCTGACTGGATGTTTGCTGTGGTATACTTCTTCAGCACTGCGGCGCAAACATCTGCCTCGCGACTCACACGTCAGCATGAATTTCATACTGCGCACAAGAGTGGTCGTCTTGAGTGGAAGGAGGTTTTTTTCCAGCAGAGAGTCATCTTTGCGCGTCCCATGAG
+

@CCCBFFGGAFGGGGFAFGDGCCAF<FFGDE<FFFGGGDFFFGCFGGFAGAGGGGGGGGDGGGGG8FFGGGGDCCG@FEG,BF+BDFEFGFFGA,@FFAFGFF,ECG:=F@,AEFGFGGG>FC+,@,,,6,8,6D>C+=>?E+=3,@,,3,@+6@AD@,7,7<,,;C+1773EF*2@

I tried installing ABySS vs. 1.5.2 on both a Mac Pro and a Linux (Ubuntu) Server and the error happens in both cases. I use the simple command

abyss-pe v=-v k=64 name=test in='reads1.fq reads2.fq'

just to check if it's working.

Please find the output attached.

I would be very grateful if the problem could be solved!

Thank you so much,

Flo

[Ben Vandervalk]

Hi Florentine,

I noticed this line your log output:

"Read 0 alignments"

which suggests that the abyss-map command isn't producing any output.  I can't imagine why that would happen, though.

Can you run this command in your assembly directory and see if it produces any output?

$ abyss-map -v -j2 -l64 reads1.fq reads2.fq test-3.fa | head -100

Also, can you confirm all the files involved have non-zero size?

$ du -hsc reads1.fq reads2.fq test-3.fa

- Ben

--

[Ben Vandervalk]

Also, could you please provide the output of the following command:

$ abyss-pe versions

- Ben